Explain Podcast

Spinnin' bases on wafers to do mostly natural SBS

Chapters:

- 00:00 Ultima ePCR with beads

- 07:10 Spinning the wafer, nucleotides, no blocking

- 14:30 Ultima ppmSeq + Element UltraQ

- 25:30 How Element UltraQ was born

- 30:30 snakemake, cromwell, nextflow

- 36:50 ncRNA

Ultimas homepage: https://www.ultimagenomics.com/

Nature paper with the chemistry: https://www.nature.com/articles/s41587-022-01452-6

Elements UltraQ chemistry:

https://www.elementbiosciences.com/cloudbreak-ultraq-enhanced-sequencing-accuracy-when-precision-matters-most

Snakemake: https://snakemake.readthedocs.io/en/stable/

Nextflow: https://www.nextflow.io/docs/latest/index.html

Cromwell: https://cromwell.readthedocs.io/en/stable/

Small overview of not all ncRNA types: https://microbenotes.com/types-of-rna/

Since 2018, West German Genome Center (https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) – network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Because sometimes a jellyfish prevents quenching

Chapters:

01:00 - XLeap update from Illumina

08:00 - Avidites start, splitting the problems

13:20 - In-depth comparison to Illumina

22:00 - Element summary

23:30 - Bioinformatics tools: Jellyfish, KAT

25:00 - QuickGen: GWAS

Illumina about their XLeap: https://www.illumina.com/science/genomics-research/articles/data-quality-q-scores.html

Sandiegomics about element: https://sandiegomics.com/element-beats-illumina-to-the-200-genome/

Nature paper about the chemistry: https://www.nature.com/articles/s41587-023-01750-7

Jellyfish for k-mer counting: https://github.com/gmarcais/Jellyfish

GWAS Catalog: very nice data collection: https://www.ebi.ac.uk/gwas/diagram

Correcting population-based GWAS bias: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011242

Since 2018, West German Genome Center (https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Now Illuminas IP, previously PacBios, previously OMNIONE...

Because only one type of nucleotide is not complicated enough

Chapters:

01:35 Introducing old problems

15:30 More Phred, more better

34:40 QuickGen: genetic testing

47:40 Bioinformatics tools: samtools

PacBio ONSO Specs: https://www.pacb.com/wp-content/uploads/Onso-specification-sheet.pdf

SBB explained by PacBio: https://www.pacb.com/blog/sbb-sequencing/

Why higher quality is better: https://pmc.ncbi.nlm.nih.gov/articles/PMC11331594/

Short read sequencing market heating up: https://www.nature.com/articles/s41587-022-01632-4

SBB for visual learners: https://www.youtube.com/watch?v=i_mSaNBOVmQ

Since 2018, West German Genome Center (https://wggc.de/)operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Mixing up long and cheap

... soon we need to add "vs mid-reads"

Chapters:

00:00:00 Intro

00:03:30 Florians history

00:13:50 Q&A Ressources for Bioinformatics

00:27:00 Long-read-tools.org

00:35:42 ONT || PacBio

00:57:00 Storage

01:09:00 Outro

Up-to-date, raw prices:https://albertvilella.substack.com/p/march-2024-ngsspecs-update

Dovetail comparing the two long-read technologies:https://dovetailbiopartners.com/2023/08/10/pacbio-vs-nanopore-unraveling-the-sequencing-odyssey-in-life-sciences/

Comparing PacBios old CLRs to ONT:https://academic.oup.com/g3journal/article/12/11/jkac192/6651842?login=true

RNA Performance comparison, wonderful read:https://www.biorxiv.org/content/10.1101/2023.07.25.550582v1.full.pdf+html

Integras 0.02$:https://www.integra-biosciences.com/united-states/en/blog/article/short-read-vs-long-read-sequencing

Since 2018, West German Genome Center (https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).

Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903)

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Rolling in circles to make DNA yarns

Chapters:

00:00 Bioinformatics Upper Crust Tools

04:04 STAR

05:00 MGI

15:00 Daniels first contact

20:00 Brief Market Overview

22:30 Short read market

26:00 DFG High Costs Sequencing Projects Application

29:20 QuickGen: Introns and Exons

35:00 Conclusion

MGI vs Illumina: https://alitheagenomics.com/blog/how-do-rna-seq-results-compare-between-illumina-and-mgi-sequencing-platforms

Rolling the circle: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568012/pdf/nihms894568.pdf

MGI vs Illumina legal case:https://www.reuters.com/technology/illumina-ordered-pay-chinese-company-333-million-gene-sequencing-patent-case-2022-05-06/

The basics of MGIs technology: https://www.youtube.com/watch?v=gThcHHh4R0w

DFG Application:https://www.dfg.de/de/aktuelles/neuigkeiten-themen/info-wissenschaft/2024/ifw-24-30

GTL/WGGC: https://www.gtl.hhu.de/wggc

TSM link http://tsm.gtl.hhu.de/- submit your request and our colleagues will contact you

Since 2018, West German Genome Center https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany.

Listen to our podcast and we're happy to receive yourfeedback&questions via Email ( podcast[dot]explain[at]gmail[dot]com ).

Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903)

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Who needs all bases anyway?

Chapters:

00:00 Phasing

08:50 Not Sequencing, really

14:00 Bionano Saphyr Chip

26:00 Nabsys - going electric

29:30 Tools available

39:00 QuickGen with Iuliia: Transposons!

Links:

Small explainer by CAP: https://www.cap.org/member-resources/articles/optical-genome-mapping-a-tool-with-significant-potential-from-discovery-to-diagnostics

What genome mapping can be used for: https://www.mdpi.com/2073-4425/12/3/398

Finding SVs with genome mapping: https://www.nature.com/articles/s41408-024-01059-x

Bionano github repos: https://github.com/search?q=bionano&type=repositories&s=updated&o=desc

Listen to our podcast and send your feedback to podcast[dot]explain[at]gmail[dot]com

Since 2019, West German Genome Center https://wggc.de/ operates as the nextgeneration sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network NGS-CN https://ngs-cn.de/ – network of NGS core facilities in Germany.

The Explain Podcast is recorded at the Multimediazentrum at Heinrich-Heine University ofDüsseldorf https://www.mmz.hhu.de/ Our podcast is an outreach activity within the national genomics facility ”West German Genome Center” funded by the Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen https://www.mkw.nrw/land-foerdert-spitzenzentrum-fuer-genomsequenzierung-nordrhein-westfalen/

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Chapters:

00:00 Gambling

15:00 Bubbles

30:00 Holes

57:30 One more thing

1:07:00 Finale

1:08:00 Finale of season 1!

Eric Chow explaining single cell sequencing: https://www.youtube.com/watch?v=k9VFNLLQP8c

Overview of things to consider: https://www.youtube.com/watch?v=VWUPKrnRvoQ

How to analyze single cell data: https://www.youtube.com/watch?v=5HBzgsz8qyk

A very good single cell analysis toolkit: https://satijalab.org/seurat/

Explainer for the rough workflow:https://www.technologynetworks.com/genomics/articles/understanding-single-cell-sequencing-how-it-works-and-its-applications-357578

Quick explainer on single cell sequencing:https://www.the-scientist.com/single-cell-sequencing-in-a-nutshell-71048

A method-overview paper: https://www.nature.com/articles/s12276-020-00499-2

Comparing BD Parse and 10xGenomics: https://pubmed.ncbi.nlm.nih.gov/33414681/

Pseudotime analysis: https://bioconductor.org/books/3.14/OSCA.advanced/trajectory-analysis.html

Since 2018, West German Genome Center (https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany.

Listen to our podcast and send your feedback to ( podcast[dot]explain[at]gmail[dot]com ).

The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903).

PS: I do not know how in the Parse approach the cells are treated to let the ligase and DNA enter each cell, but do not let RNA flow out of the cell at the same time. -DR

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Getting the most out of Machines

Chapters:

00:00 PhiX

14:30 low complexity

19:30 UMIs

32:10 FastQC

43:00 MultiQC

56:40 PycoQC

PhiX concentrations for loading a validation run:https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001536

Dnatech on why UMIs are used:https://dnatech.genomecenter.ucdavis.edu/faqs/what-are-umis-and-why-are-they-used-in-high-throughput-sequencing/

BMH learning on UMIs: https://www.youtube.com/watch?v=sRPMsnhIBK0

FastQC for QC of .fastq(.gz) files:https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

A FastQC report from a „good“ sample:https://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc.html

multiqc for summarizing QC reports: https://multiqc.info/

UMI-tools for working with UMI data: https://umi-tools.readthedocs.io/en/latest/

pycoQC for Nanopore QC: https://github.com/a-slide/pycoQC

Since 2018, West German Genome Center (https://wggc.de/)operates as the next generation sequencing facility and supportsresearch in genomics & transcriptomics by providing expertise andsequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/)- network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).

The Explain Podcast is recorded at the Medienlabor atHeinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Pushing spaghetti through holes

Chapers:

00:00 Intro

11:15 Measuring Ions

17:00 Quality

23:00 Duplex

24:30 MinION

25:15 PromethION

28:20 Methylation

29:00 Direct RNA sequencing

38:25 Basecalling

46:00 Basecalling bias

53:50 Sequencing proteins

- Nanopore explainer: https://nanoporetech.com/applications/dna-nanopore-sequencing

- Oxsci explaining the technology:https://oxsci.org/pore-over-this-advances-in-dna-sequencing/

- History of Nanopore:https://www.whatisbiotechnology.org/index.php/science/summary/nanopore/nanopore-sequencing-makes-it-possible-to-decode-the

- Shmou’s Biology explaining Nanopore sequencing:https://www.youtube.com/watch?v=MlluAjhzXqI

- A direct comparison of Nanopore and Illumina output:https://medresearch.umich.edu/office-research/about-office-research/biomedical-research-core-facilities/advanced-genomics-core/technologies/next-generation-sequencing

- A nice Nanopore QC tool we use: https://hpc.nih.gov/apps/pycoQC.html

- How a MinION looks like:https://www.whatech.com/og/markets-research/medical/658327-global-nanopore-sequencing-market-2020

Since 2018, West German Genome Center (https://wggc.de/)operates as the next generation sequencing facility and supportsresearch in genomics & transcriptomics by providing expertise andsequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/)- network of NGS core facilities in Germany.

Listen to our podcast and we're happy to receive your feedback&questions via Email ( podcast[dot]explain[at]gmail[dot]com ).

The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/).

Our podcast is an outreach activity within the national genomicsfacility "West German Genome Center" funded by the DFG(https://www.dfg.de/) (No. 407493903).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Zipping rounds in zeptoliters

Chapters:

00:00 Intro

07:00 Laser

09:00 Zeptoliters

13:30 Polymerase speed

19:00 Error rate

22:00 SMRT Cell

25:45 ccs

30:00 Fragment size

34:30 Megaruptor

38:20 Data flow

47:00 SVs

53:00 MAS Seq

- Starter: https://www.nature.com/articles/s41366-021-00824-3

- Karobben on PacBio sequencing: https://karobben.github.io/2023/10/30/Bioinfor/PacBio/

- bioinformticamente explaining the technology:https://bioinformaticamente.com/2020/12/05/pacbio-sequencing/

- Basic Biochem explainer of SMRT sequencing:https://www.youtube.com/watch?v=H2gUmRf-K1c

- Genomics Lab explaining it: https://www.youtube.com/watch?v=vRhUSjhygDU

- PacBio explaining BAM Tags: https://pacbiofileformats.readthedocs.io/en/13.0/BAM.html

- Megaruptor3 explainer (how we make the right sized fragments) :https://www.youtube.com/watch?v=zVhqnkQL8zo

- How we select the right sized fragments: https://www.youtube.com/watch?v=A25C8xfBbq8

Since 2018, West German Genome Center (https://wggc.de/)operates as the next generation sequencing facility and supportsresearch in genomics & transcriptomics by providing expertise andsequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/)- network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).

The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/).

Our podcast is an outreach activity within the national genomicsfacility "West German Genome Center" funded by the DFG(https://www.dfg.de/) (No. 407493903).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠